library(here)
library(galah)
library(skimr)
library(dplyr)
library(lubridate)
library(stringr)
library(ggplot2)
library(leaflet)
library(leaflet.extras)
library(reactable)
library(scico)
reptilia <- readRDS(here("data", "reptilia"))
reptilia_tidy <- reptilia %>%
filter(cl22 == "Australian Capital Territory") %>%
rename(state = cl22,
forestType = cl10902) %>%
mutate(forestType = na_if(forestType, ""),
basisOfRecord = tolower(basisOfRecord),
basisOfRecord = str_replace(basisOfRecord, "_", " "),
eventDate = as_datetime(eventDate, tz = "Australia/Sydney", format = NULL),
eventDate = as_date(eventDate, tz = NULL),
month = month(eventDate))
skim(reptilia_tidy)
| Name | reptilia_tidy |
| Number of rows | 10145 |
| Number of columns | 12 |
| _______________________ | |
| Column type frequency: | |
| character | 8 |
| Date | 1 |
| numeric | 3 |
| ________________________ | |
| Group variables | None |
Variable type: character
| skim_variable | n_missing | complete_rate | min | max | empty | n_unique | whitespace |
|---|---|---|---|---|---|---|---|
| scientificName | 0 | 1 | 4 | 33 | 0 | 102 | 0 |
| genus | 0 | 1 | 0 | 16 | 106 | 52 | 0 |
| family | 0 | 1 | 0 | 15 | 38 | 12 | 0 |
| order | 0 | 1 | 0 | 10 | 4 | 3 | 0 |
| dataResourceName | 0 | 1 | 9 | 87 | 0 | 23 | 0 |
| basisOfRecord | 0 | 1 | 7 | 18 | 0 | 5 | 0 |
| state | 0 | 1 | 28 | 28 | 0 | 1 | 0 |
| forestType | 17 | 1 | 6 | 31 | 0 | 10 | 0 |
Variable type: Date
| skim_variable | n_missing | complete_rate | min | max | median | n_unique |
|---|---|---|---|---|---|---|
| eventDate | 5206 | 0.49 | 1954-01-22 | 2021-11-25 | 2012-10-08 | 1783 |
Variable type: numeric
| skim_variable | n_missing | complete_rate | mean | sd | p0 | p25 | p50 | p75 | p100 | hist |
|---|---|---|---|---|---|---|---|---|---|---|
| decimalLatitude | 0 | 1.00 | -35.34 | 0.15 | -35.91 | -35.40 | -35.3 | -35.24 | -35.12 | ▁▁▃▇▇ |
| decimalLongitude | 0 | 1.00 | 149.11 | 0.30 | 148.76 | 148.99 | 149.1 | 149.15 | 150.77 | ▇▂▁▁▁ |
| month | 5206 | 0.49 | 7.92 | 3.92 | 1.00 | 3.00 | 10.0 | 11.00 | 12.00 | ▃▁▁▂▇ |
# remove cols not of interest in a table
reptilia_subset <- reptilia_tidy %>%
select(eventDate:basisOfRecord, forestType)
reactable(
reptilia_subset,
columns = list(
eventDate = colDef(name = "Date"),
scientificName = colDef(name = "Species"),
genus = colDef(name = "Genus"),
family = colDef(name = "Family"),
order = colDef(name = "Order"),
dataResourceName = colDef(name = "Source"),
basisOfRecord = colDef(name = "Record type"),
forestType = colDef(name = "Forest type")
),
showSortable = TRUE,
filterable = TRUE,
searchable = TRUE,
showPageInfo = FALSE,
striped = TRUE
)
ALA occurrence download https://doi.org/10.26197/ala.1999d964-1ccc-44f5-8cba-ed7ec33b1e41. Accessed from R with galah 1.3.1 (https://github.com/AtlasOfLivingAustralia/galah/) on 2021-12-04.